Starting phenix.real_space_refine on Fri Mar 6 03:24:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lez_23295/03_2026/7lez_23295.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lez_23295/03_2026/7lez_23295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lez_23295/03_2026/7lez_23295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lez_23295/03_2026/7lez_23295.map" model { file = "/net/cci-nas-00/data/ceres_data/7lez_23295/03_2026/7lez_23295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lez_23295/03_2026/7lez_23295.cif" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 92 5.16 5 C 17562 2.51 5 N 4710 2.21 5 O 5418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27794 Number of models: 1 Model: "" Number of chains: 20 Chain: "D" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "B" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "P" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "N" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "J" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "G" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1692 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.94, per 1000 atoms: 0.21 Number of scatterers: 27794 At special positions: 0 Unit cell: (163.28, 132.08, 153.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 92 16.00 O 5418 8.00 N 4710 7.00 C 17562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 152 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 152 " - pdb=" SG CYS Q 207 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 977.9 milliseconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6620 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 50 sheets defined 26.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.115A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.849A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN A 143 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 285 through 304 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.731A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 279 through 283' Processing helix chain 'B' and resid 285 through 304 Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.662A pdb=" N GLN C 143 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.606A pdb=" N HIS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 283' Processing helix chain 'C' and resid 285 through 304 Processing helix chain 'P' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 128 Processing helix chain 'P' and resid 183 through 188 Processing helix chain 'O' and resid 79 through 83 removed outlier: 4.114A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 128 Processing helix chain 'O' and resid 183 through 188 Processing helix chain 'M' and resid 23 through 26 Processing helix chain 'M' and resid 27 through 34 Processing helix chain 'M' and resid 35 through 41 Processing helix chain 'M' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL M 73 " --> pdb=" O ASN M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 143 removed outlier: 3.662A pdb=" N GLN M 143 " --> pdb=" O LEU M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 149 removed outlier: 3.731A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 207 Processing helix chain 'M' and resid 207 through 220 Processing helix chain 'M' and resid 253 through 267 Processing helix chain 'M' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU M 282 " --> pdb=" O ASN M 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY M 283 " --> pdb=" O PRO M 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 279 through 283' Processing helix chain 'M' and resid 285 through 304 Processing helix chain 'N' and resid 23 through 26 Processing helix chain 'N' and resid 27 through 34 Processing helix chain 'N' and resid 35 through 41 Processing helix chain 'N' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL N 73 " --> pdb=" O ASN N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 102 No H-bonds generated for 'chain 'N' and resid 100 through 102' Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN N 143 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS N 187 " --> pdb=" O ASP N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 207 Processing helix chain 'N' and resid 207 through 220 Processing helix chain 'N' and resid 253 through 267 Processing helix chain 'N' and resid 279 through 283 removed outlier: 3.620A pdb=" N LEU N 282 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY N 283 " --> pdb=" O PRO N 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 279 through 283' Processing helix chain 'N' and resid 285 through 304 Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 35 through 41 Processing helix chain 'J' and resid 69 through 90 removed outlier: 3.848A pdb=" N VAL J 73 " --> pdb=" O ASN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 102 No H-bonds generated for 'chain 'J' and resid 100 through 102' Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.793A pdb=" N HIS J 111 " --> pdb=" O SER J 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 removed outlier: 3.663A pdb=" N GLN J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.730A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 193 removed outlier: 3.607A pdb=" N HIS J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 267 Processing helix chain 'J' and resid 279 through 283 removed outlier: 3.619A pdb=" N LEU J 282 " --> pdb=" O ASN J 279 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY J 283 " --> pdb=" O PRO J 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 279 through 283' Processing helix chain 'J' and resid 285 through 304 Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.161A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR D 69 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.707A pdb=" N VAL D 148 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 152 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.707A pdb=" N VAL D 148 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 152 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 192 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR D 188 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS D 207 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG E 45 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS E 134 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 176 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 162 " --> pdb=" O SER E 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AB2, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS E 149 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG I 45 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.707A pdb=" N CYS I 134 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER I 176 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER I 162 " --> pdb=" O SER I 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'I' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS I 149 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR I 193 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE A 8 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR A 50 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE A 10 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 52 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 12 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 94 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE A 275 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 96 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 174 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE A 198 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR A 176 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE B 8 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR B 50 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE B 10 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 52 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY B 12 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 94 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE B 275 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 96 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE B 174 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE B 198 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B 176 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE C 8 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 50 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE C 10 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP C 52 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY C 12 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER C 94 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE C 275 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL C 96 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE C 174 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE C 198 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C 176 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AC3, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR P 87 " --> pdb=" O TYR P 36 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG P 45 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS P 134 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER P 176 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER P 162 " --> pdb=" O SER P 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'P' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS P 149 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR P 193 " --> pdb=" O LYS P 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.839A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR O 87 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG O 45 " --> pdb=" O GLN O 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 116 through 118 removed outlier: 3.708A pdb=" N CYS O 134 " --> pdb=" O SER O 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER O 176 " --> pdb=" O SER O 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER O 162 " --> pdb=" O SER O 176 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 129 through 130 Processing sheet with id=AD2, first strand: chain 'O' and resid 147 through 150 removed outlier: 3.860A pdb=" N LYS O 149 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR O 193 " --> pdb=" O LYS O 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE M 8 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR M 50 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE M 10 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP M 52 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY M 12 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER M 94 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE M 275 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL M 96 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL M 120 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE M 177 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP M 122 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE M 174 " --> pdb=" O LYS M 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE M 198 " --> pdb=" O ILE M 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR M 176 " --> pdb=" O PHE M 198 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE N 8 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR N 50 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE N 10 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP N 52 " --> pdb=" O ILE N 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY N 12 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER N 94 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE N 275 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL N 96 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL N 120 " --> pdb=" O VAL N 175 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE N 177 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP N 122 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE N 174 " --> pdb=" O LYS N 196 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE N 198 " --> pdb=" O ILE N 174 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR N 176 " --> pdb=" O PHE N 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.794A pdb=" N ILE J 8 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR J 50 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE J 10 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP J 52 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY J 12 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER J 94 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE J 275 " --> pdb=" O SER J 94 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL J 96 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL J 120 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE J 177 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TRP J 122 " --> pdb=" O ILE J 177 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE J 174 " --> pdb=" O LYS J 196 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE J 198 " --> pdb=" O ILE J 174 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR J 176 " --> pdb=" O PHE J 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.162A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL G 148 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 152 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL G 148 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 152 " --> pdb=" O SER G 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 192 " --> pdb=" O CYS G 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR G 188 " --> pdb=" O GLY G 156 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 163 through 166 removed outlier: 3.739A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 3 through 7 removed outlier: 4.162A pdb=" N GLN R 3 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER R 25 " --> pdb=" O GLN R 3 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 45 through 50 removed outlier: 6.289A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'R' and resid 69 through 72 removed outlier: 3.866A pdb=" N THR R 69 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL R 148 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 152 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL R 148 " --> pdb=" O THR R 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 152 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER R 192 " --> pdb=" O CYS R 152 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR R 188 " --> pdb=" O GLY R 156 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS R 207 " --> pdb=" O LYS R 220 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 3 through 7 removed outlier: 4.161A pdb=" N GLN Q 3 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER Q 25 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 45 through 50 removed outlier: 6.288A pdb=" N TRP Q 36 " --> pdb=" O MET Q 48 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 69 through 72 removed outlier: 3.867A pdb=" N THR Q 69 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL Q 148 " --> pdb=" O THR Q 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS Q 152 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 132 through 133 removed outlier: 3.708A pdb=" N VAL Q 148 " --> pdb=" O THR Q 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS Q 152 " --> pdb=" O SER Q 192 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 192 " --> pdb=" O CYS Q 152 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR Q 188 " --> pdb=" O GLY Q 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 163 through 166 removed outlier: 3.740A pdb=" N CYS Q 207 " --> pdb=" O LYS Q 220 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.07 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8627 1.34 - 1.46: 4917 1.46 - 1.57: 14736 1.57 - 1.69: 4 1.69 - 1.81: 130 Bond restraints: 28414 Sorted by residual: bond pdb=" CA SER G 77 " pdb=" C SER G 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.81e+01 bond pdb=" CA SER R 77 " pdb=" C SER R 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.79e+01 bond pdb=" CA SER D 77 " pdb=" C SER D 77 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.34e-02 5.57e+03 1.78e+01 bond pdb=" CA SER Q 77 " pdb=" C SER Q 77 " ideal model delta sigma weight residual 1.523 1.579 -0.056 1.34e-02 5.57e+03 1.75e+01 bond pdb=" C VAL N 165 " pdb=" N THR N 166 " ideal model delta sigma weight residual 1.333 1.289 0.045 1.61e-02 3.86e+03 7.71e+00 ... (remaining 28409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 37592 3.09 - 6.19: 900 6.19 - 9.28: 144 9.28 - 12.38: 8 12.38 - 15.47: 12 Bond angle restraints: 38656 Sorted by residual: angle pdb=" CA TYR I 49 " pdb=" CB TYR I 49 " pdb=" CG TYR I 49 " ideal model delta sigma weight residual 113.90 126.47 -12.57 1.80e+00 3.09e-01 4.88e+01 angle pdb=" CA TYR E 49 " pdb=" CB TYR E 49 " pdb=" CG TYR E 49 " ideal model delta sigma weight residual 113.90 126.45 -12.55 1.80e+00 3.09e-01 4.86e+01 angle pdb=" CA TYR O 49 " pdb=" CB TYR O 49 " pdb=" CG TYR O 49 " ideal model delta sigma weight residual 113.90 126.44 -12.54 1.80e+00 3.09e-01 4.85e+01 angle pdb=" CA TYR P 49 " pdb=" CB TYR P 49 " pdb=" CG TYR P 49 " ideal model delta sigma weight residual 113.90 126.41 -12.51 1.80e+00 3.09e-01 4.83e+01 angle pdb=" N ARG P 54 " pdb=" CA ARG P 54 " pdb=" C ARG P 54 " ideal model delta sigma weight residual 110.91 118.47 -7.56 1.17e+00 7.31e-01 4.17e+01 ... (remaining 38651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.78: 15385 12.78 - 25.56: 1261 25.56 - 38.33: 300 38.33 - 51.11: 48 51.11 - 63.89: 24 Dihedral angle restraints: 17018 sinusoidal: 6620 harmonic: 10398 Sorted by residual: dihedral pdb=" CA PRO R 135 " pdb=" C PRO R 135 " pdb=" N LEU R 136 " pdb=" CA LEU R 136 " ideal model delta harmonic sigma weight residual 180.00 123.79 56.21 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA PRO D 135 " pdb=" C PRO D 135 " pdb=" N LEU D 136 " pdb=" CA LEU D 136 " ideal model delta harmonic sigma weight residual 180.00 123.83 56.17 0 5.00e+00 4.00e-02 1.26e+02 dihedral pdb=" CA PRO G 135 " pdb=" C PRO G 135 " pdb=" N LEU G 136 " pdb=" CA LEU G 136 " ideal model delta harmonic sigma weight residual 180.00 123.83 56.17 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 17015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3317 0.067 - 0.133: 880 0.133 - 0.200: 180 0.200 - 0.267: 17 0.267 - 0.333: 10 Chirality restraints: 4404 Sorted by residual: chirality pdb=" CB ILE M 129 " pdb=" CA ILE M 129 " pdb=" CG1 ILE M 129 " pdb=" CG2 ILE M 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB ILE J 129 " pdb=" CA ILE J 129 " pdb=" CG1 ILE J 129 " pdb=" CG2 ILE J 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB ILE C 129 " pdb=" CA ILE C 129 " pdb=" CG1 ILE C 129 " pdb=" CG2 ILE C 129 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4401 not shown) Planarity restraints: 4960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS R 13 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO R 14 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO R 14 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO R 14 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 13 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO Q 14 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO Q 14 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO Q 14 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.079 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO D 14 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.066 5.00e-02 4.00e+02 ... (remaining 4957 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.98: 16 1.98 - 2.71: 1582 2.71 - 3.44: 40305 3.44 - 4.17: 73692 4.17 - 4.90: 122303 Nonbonded interactions: 237898 Sorted by model distance: nonbonded pdb=" ND1 HIS M 101 " pdb="MN MN M1001 " model vdw 1.255 2.400 nonbonded pdb=" ND1 HIS A 101 " pdb="MN MN A1001 " model vdw 1.255 2.400 nonbonded pdb=" CE1 HIS M 101 " pdb="MN MN M1001 " model vdw 1.368 2.540 nonbonded pdb=" CE1 HIS A 101 " pdb="MN MN A1001 " model vdw 1.368 2.540 nonbonded pdb=" ND1 HIS B 101 " pdb="MN MN B1001 " model vdw 1.437 2.400 ... (remaining 237893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'R' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'P' selection = chain 'O' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'M' selection = chain 'N' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.450 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28430 Z= 0.330 Angle : 1.200 15.475 38688 Z= 0.670 Chirality : 0.064 0.333 4404 Planarity : 0.010 0.121 4960 Dihedral : 10.277 63.891 10350 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.66 % Allowed : 10.12 % Favored : 89.22 % Rotamer: Outliers : 0.91 % Allowed : 2.60 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 3.48 % Twisted General : 1.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.35 (0.12), residues: 3618 helix: -2.73 (0.13), residues: 828 sheet: -3.13 (0.15), residues: 914 loop : -2.80 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 188 TYR 0.049 0.004 TYR P 49 PHE 0.043 0.005 PHE I 118 TRP 0.041 0.004 TRP Q 111 HIS 0.029 0.005 HIS Q 109 Details of bonding type rmsd covalent geometry : bond 0.00690 (28414) covalent geometry : angle 1.19984 (38656) SS BOND : bond 0.00294 ( 16) SS BOND : angle 1.67931 ( 32) hydrogen bonds : bond 0.21511 ( 848) hydrogen bonds : angle 9.60693 ( 2340) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 717 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8100 (ptm) cc_final: 0.7550 (ptt) REVERT: D 187 TYR cc_start: 0.8593 (m-80) cc_final: 0.8323 (m-80) REVERT: D 205 ILE cc_start: 0.7723 (mt) cc_final: 0.7020 (mm) REVERT: E 117 ILE cc_start: 0.6738 (tt) cc_final: 0.5528 (tt) REVERT: E 181 LEU cc_start: 0.8315 (mt) cc_final: 0.7538 (mp) REVERT: E 195 GLU cc_start: 0.9371 (tt0) cc_final: 0.9102 (tm-30) REVERT: I 93 LEU cc_start: 0.8010 (tm) cc_final: 0.7652 (tt) REVERT: A 95 LEU cc_start: 0.8912 (tp) cc_final: 0.8581 (tp) REVERT: A 172 LYS cc_start: 0.7628 (pttm) cc_final: 0.7101 (tttp) REVERT: A 186 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7454 (mp0) REVERT: B 28 PRO cc_start: 0.8627 (Cg_exo) cc_final: 0.8269 (Cg_endo) REVERT: B 95 LEU cc_start: 0.8740 (tp) cc_final: 0.8445 (tp) REVERT: B 304 PHE cc_start: 0.7913 (m-80) cc_final: 0.6499 (m-80) REVERT: C 200 MET cc_start: 0.7690 (mmm) cc_final: 0.7445 (mmm) REVERT: C 202 GLU cc_start: 0.7920 (mp0) cc_final: 0.7394 (mp0) REVERT: C 218 TYR cc_start: 0.7603 (t80) cc_final: 0.7222 (t80) REVERT: C 231 PHE cc_start: 0.8460 (t80) cc_final: 0.8105 (t80) REVERT: P 175 MET cc_start: 0.2291 (ttp) cc_final: 0.1682 (ptm) REVERT: P 213 GLU cc_start: 0.6646 (tt0) cc_final: 0.6270 (tt0) REVERT: O 61 ARG cc_start: 0.4663 (ptt-90) cc_final: 0.4067 (ptt90) REVERT: O 94 LEU cc_start: 0.8015 (tt) cc_final: 0.7753 (mt) REVERT: O 213 GLU cc_start: 0.7784 (tt0) cc_final: 0.7294 (tm-30) REVERT: M 66 ILE cc_start: 0.5618 (mm) cc_final: 0.5357 (tt) REVERT: M 111 HIS cc_start: 0.1579 (t-170) cc_final: 0.1260 (t-170) REVERT: M 174 ILE cc_start: 0.6607 (tt) cc_final: 0.6031 (tt) REVERT: M 195 ILE cc_start: 0.4134 (mt) cc_final: 0.3815 (mp) REVERT: M 197 TYR cc_start: 0.6636 (p90) cc_final: 0.5939 (p90) REVERT: M 213 GLU cc_start: 0.8645 (tt0) cc_final: 0.8353 (tm-30) REVERT: M 265 TYR cc_start: 0.6803 (t80) cc_final: 0.6599 (t80) REVERT: M 304 PHE cc_start: 0.2448 (m-80) cc_final: 0.1120 (m-80) REVERT: N 64 PHE cc_start: 0.5465 (t80) cc_final: 0.5198 (t80) REVERT: N 158 ASP cc_start: 0.7680 (m-30) cc_final: 0.7382 (t0) REVERT: N 198 PHE cc_start: 0.6686 (m-80) cc_final: 0.6439 (m-80) REVERT: N 200 MET cc_start: 0.1671 (mmm) cc_final: 0.0562 (mmm) REVERT: N 282 LEU cc_start: 0.1774 (mt) cc_final: 0.1009 (tt) REVERT: J 200 MET cc_start: 0.6658 (mmm) cc_final: 0.6184 (tpp) REVERT: J 262 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6679 (mm-30) REVERT: J 276 MET cc_start: -0.0432 (mmt) cc_final: -0.0764 (mmt) REVERT: G 37 VAL cc_start: 0.7313 (OUTLIER) cc_final: 0.6704 (t) REVERT: G 164 LEU cc_start: 0.8714 (mt) cc_final: 0.8435 (tp) REVERT: R 67 ARG cc_start: 0.6396 (mtm110) cc_final: 0.5427 (mtp-110) REVERT: R 158 PHE cc_start: 0.8701 (t80) cc_final: 0.8390 (t80) REVERT: R 187 TYR cc_start: 0.8306 (m-80) cc_final: 0.7910 (m-80) REVERT: Q 125 SER cc_start: 0.2519 (OUTLIER) cc_final: 0.1789 (p) REVERT: Q 167 ASN cc_start: 0.7307 (m-40) cc_final: 0.7102 (m110) outliers start: 28 outliers final: 4 residues processed: 743 average time/residue: 0.2133 time to fit residues: 234.8221 Evaluate side-chains 344 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 338 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN A 90 ASN ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN B 141 HIS B 312 HIS C 90 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 126 HIS C 139 ASN C 187 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN ** P 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN O 137 ASN O 189 HIS ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 126 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 ASN N 294 ASN ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN J 43 GLN J 90 ASN J 141 HIS J 187 HIS ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 109 HIS G 110 ASN G 167 ASN R 6 GLN R 55 ASN R 57 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 31 ASN Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 HIS ** Q 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.126362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099166 restraints weight = 121830.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.095737 restraints weight = 124994.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.096384 restraints weight = 91171.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.096945 restraints weight = 63736.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.097072 restraints weight = 55541.847| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 28430 Z= 0.272 Angle : 0.910 11.901 38688 Z= 0.469 Chirality : 0.052 0.265 4404 Planarity : 0.008 0.107 4960 Dihedral : 8.075 63.533 3920 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.87 % Favored : 89.80 % Rotamer: Outliers : 0.26 % Allowed : 3.24 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.13), residues: 3618 helix: -1.33 (0.16), residues: 796 sheet: -2.55 (0.16), residues: 856 loop : -2.35 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 87 TYR 0.035 0.003 TYR O 49 PHE 0.036 0.003 PHE O 118 TRP 0.033 0.003 TRP G 50 HIS 0.012 0.003 HIS P 91 Details of bonding type rmsd covalent geometry : bond 0.00617 (28414) covalent geometry : angle 0.90971 (38656) SS BOND : bond 0.00803 ( 16) SS BOND : angle 1.41004 ( 32) hydrogen bonds : bond 0.04993 ( 848) hydrogen bonds : angle 6.77712 ( 2340) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 433 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.7828 (ptm) cc_final: 0.7576 (ptm) REVERT: D 93 VAL cc_start: 0.5779 (t) cc_final: 0.5553 (p) REVERT: D 99 GLU cc_start: 0.7375 (tt0) cc_final: 0.6767 (tt0) REVERT: E 4 MET cc_start: 0.7150 (tpt) cc_final: 0.6914 (tpt) REVERT: E 134 CYS cc_start: 0.1585 (t) cc_final: 0.0352 (t) REVERT: E 136 LEU cc_start: 0.7814 (mp) cc_final: 0.6962 (mp) REVERT: E 187 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8659 (mm-30) REVERT: I 175 MET cc_start: 0.5440 (ttp) cc_final: 0.5081 (ttm) REVERT: A 172 LYS cc_start: 0.7702 (pttm) cc_final: 0.7476 (ptmm) REVERT: A 206 LEU cc_start: 0.8021 (mt) cc_final: 0.7635 (mt) REVERT: A 212 MET cc_start: 0.7381 (mmm) cc_final: 0.6971 (tpp) REVERT: B 19 GLN cc_start: 0.8771 (pp30) cc_final: 0.8281 (pp30) REVERT: B 128 ASP cc_start: 0.8862 (m-30) cc_final: 0.8547 (m-30) REVERT: C 77 SER cc_start: 0.9077 (m) cc_final: 0.8802 (p) REVERT: C 172 LYS cc_start: 0.7221 (pttm) cc_final: 0.6872 (mttp) REVERT: C 276 MET cc_start: 0.8567 (mpp) cc_final: 0.7674 (mtt) REVERT: P 103 LYS cc_start: 0.7570 (tptp) cc_final: 0.7211 (tppt) REVERT: O 81 GLU cc_start: 0.8361 (pt0) cc_final: 0.8112 (pt0) REVERT: O 175 MET cc_start: 0.3133 (ptm) cc_final: 0.2668 (tmm) REVERT: O 213 GLU cc_start: 0.7642 (tt0) cc_final: 0.7061 (tm-30) REVERT: M 111 HIS cc_start: 0.1514 (t-170) cc_final: 0.1128 (t-170) REVERT: M 265 TYR cc_start: 0.6136 (t80) cc_final: 0.5843 (t80) REVERT: M 301 LEU cc_start: 0.2667 (mt) cc_final: 0.2330 (tp) REVERT: M 304 PHE cc_start: 0.2174 (m-80) cc_final: 0.1943 (m-10) REVERT: N 176 TYR cc_start: 0.4207 (m-80) cc_final: 0.3627 (m-80) REVERT: J 97 LEU cc_start: 0.3254 (pp) cc_final: 0.2962 (mt) REVERT: R 62 GLN cc_start: 0.8778 (mp10) cc_final: 0.8505 (pp30) REVERT: R 155 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8391 (ttmt) REVERT: Q 155 LYS cc_start: 0.7897 (mttt) cc_final: 0.7438 (mttt) outliers start: 8 outliers final: 3 residues processed: 441 average time/residue: 0.2096 time to fit residues: 140.3144 Evaluate side-chains 262 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 283 optimal weight: 0.0770 chunk 282 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 340 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 79 GLN A 311 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 126 HIS C 228 HIS C 312 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 124 GLN ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 90 GLN ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 ASN N 79 GLN ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN R 43 GLN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.126620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.099740 restraints weight = 121741.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.096387 restraints weight = 128012.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.097270 restraints weight = 85562.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.097495 restraints weight = 62865.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.097831 restraints weight = 55754.401| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28430 Z= 0.176 Angle : 0.771 11.600 38688 Z= 0.396 Chirality : 0.049 0.431 4404 Planarity : 0.007 0.126 4960 Dihedral : 7.326 58.957 3920 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.65 % Favored : 90.05 % Rotamer: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.13), residues: 3618 helix: -0.80 (0.17), residues: 814 sheet: -2.15 (0.16), residues: 866 loop : -2.06 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 38 TYR 0.033 0.002 TYR O 49 PHE 0.035 0.002 PHE I 71 TRP 0.025 0.002 TRP G 50 HIS 0.011 0.002 HIS N 187 Details of bonding type rmsd covalent geometry : bond 0.00394 (28414) covalent geometry : angle 0.77076 (38656) SS BOND : bond 0.00335 ( 16) SS BOND : angle 1.02045 ( 32) hydrogen bonds : bond 0.04125 ( 848) hydrogen bonds : angle 6.13678 ( 2340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 389 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8102 (mmmm) REVERT: D 93 VAL cc_start: 0.5815 (t) cc_final: 0.5594 (p) REVERT: E 145 ASN cc_start: 0.7978 (t0) cc_final: 0.7179 (t0) REVERT: E 147 LYS cc_start: 0.7830 (mppt) cc_final: 0.7563 (mppt) REVERT: A 95 LEU cc_start: 0.9065 (tp) cc_final: 0.8845 (tp) REVERT: A 172 LYS cc_start: 0.7574 (pttm) cc_final: 0.7041 (tttp) REVERT: A 183 ASP cc_start: 0.6876 (p0) cc_final: 0.6417 (p0) REVERT: A 186 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 19 GLN cc_start: 0.8836 (pp30) cc_final: 0.8351 (pp30) REVERT: B 95 LEU cc_start: 0.8637 (tt) cc_final: 0.8312 (tp) REVERT: B 127 THR cc_start: 0.9071 (p) cc_final: 0.8586 (t) REVERT: B 276 MET cc_start: 0.8161 (mmm) cc_final: 0.7243 (mmm) REVERT: C 77 SER cc_start: 0.9080 (m) cc_final: 0.8765 (p) REVERT: C 172 LYS cc_start: 0.7220 (pttm) cc_final: 0.6596 (mttp) REVERT: P 24 ARG cc_start: 0.7300 (mtm180) cc_final: 0.7007 (mtm180) REVERT: P 98 PHE cc_start: 0.4457 (m-80) cc_final: 0.3921 (m-80) REVERT: P 175 MET cc_start: 0.3159 (ttp) cc_final: 0.2839 (tmm) REVERT: O 75 ILE cc_start: 0.6411 (mp) cc_final: 0.6156 (mm) REVERT: O 175 MET cc_start: 0.3253 (ptm) cc_final: 0.2861 (tmm) REVERT: O 213 GLU cc_start: 0.7484 (tt0) cc_final: 0.6882 (tm-30) REVERT: M 118 LEU cc_start: 0.3551 (pp) cc_final: 0.2607 (pp) REVERT: M 158 ASP cc_start: 0.6772 (t0) cc_final: 0.6361 (t0) REVERT: M 265 TYR cc_start: 0.6062 (t80) cc_final: 0.5753 (t80) REVERT: N 176 TYR cc_start: 0.4095 (m-80) cc_final: 0.3595 (m-80) REVERT: N 198 PHE cc_start: 0.5349 (m-80) cc_final: 0.4508 (m-80) REVERT: J 200 MET cc_start: 0.6711 (mmt) cc_final: 0.6182 (mmt) REVERT: J 262 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6028 (mm-30) REVERT: J 276 MET cc_start: -0.0941 (mmt) cc_final: -0.1938 (mtm) REVERT: R 62 GLN cc_start: 0.8869 (mp10) cc_final: 0.8648 (pp30) REVERT: Q 155 LYS cc_start: 0.7847 (mttt) cc_final: 0.7646 (mttt) outliers start: 2 outliers final: 1 residues processed: 391 average time/residue: 0.1960 time to fit residues: 117.2243 Evaluate side-chains 261 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 75 optimal weight: 0.0670 chunk 286 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 79 GLN A 141 HIS ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** N 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Q 109 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.125956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.096489 restraints weight = 110994.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.093266 restraints weight = 97943.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093443 restraints weight = 74521.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.093691 restraints weight = 57973.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.094875 restraints weight = 49098.443| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28430 Z= 0.155 Angle : 0.740 9.932 38688 Z= 0.379 Chirality : 0.048 0.276 4404 Planarity : 0.007 0.115 4960 Dihedral : 6.956 52.078 3920 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.48 % Favored : 90.24 % Rotamer: Outliers : 0.13 % Allowed : 2.56 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.14), residues: 3618 helix: -0.46 (0.18), residues: 814 sheet: -1.65 (0.18), residues: 770 loop : -1.90 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 38 TYR 0.034 0.002 TYR O 49 PHE 0.028 0.002 PHE P 71 TRP 0.024 0.002 TRP G 50 HIS 0.013 0.001 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00351 (28414) covalent geometry : angle 0.73918 (38656) SS BOND : bond 0.00352 ( 16) SS BOND : angle 1.37937 ( 32) hydrogen bonds : bond 0.03662 ( 848) hydrogen bonds : angle 5.85386 ( 2340) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 365 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7175 (ptm) cc_final: 0.6602 (ptm) REVERT: D 93 VAL cc_start: 0.5796 (t) cc_final: 0.5507 (p) REVERT: D 225 ARG cc_start: 0.4185 (pmt-80) cc_final: 0.3808 (ptp90) REVERT: E 115 VAL cc_start: 0.7023 (t) cc_final: 0.6735 (t) REVERT: E 117 ILE cc_start: 0.7496 (tt) cc_final: 0.6872 (tp) REVERT: E 145 ASN cc_start: 0.7835 (t0) cc_final: 0.7082 (t0) REVERT: E 147 LYS cc_start: 0.7723 (mppt) cc_final: 0.7449 (mppt) REVERT: I 175 MET cc_start: 0.6181 (tmm) cc_final: 0.5346 (ttm) REVERT: A 95 LEU cc_start: 0.8728 (tp) cc_final: 0.8501 (tp) REVERT: A 172 LYS cc_start: 0.7371 (pttm) cc_final: 0.6928 (tttp) REVERT: B 15 PHE cc_start: 0.7211 (t80) cc_final: 0.6413 (t80) REVERT: B 19 GLN cc_start: 0.8815 (pp30) cc_final: 0.8307 (pp30) REVERT: B 95 LEU cc_start: 0.8807 (tt) cc_final: 0.8442 (tp) REVERT: C 77 SER cc_start: 0.8996 (m) cc_final: 0.8769 (p) REVERT: C 143 GLN cc_start: 0.7768 (mt0) cc_final: 0.6874 (mt0) REVERT: C 172 LYS cc_start: 0.7017 (pttm) cc_final: 0.6725 (mttp) REVERT: P 24 ARG cc_start: 0.7415 (mtm180) cc_final: 0.7100 (mtm180) REVERT: O 75 ILE cc_start: 0.6659 (mp) cc_final: 0.6265 (mm) REVERT: O 175 MET cc_start: 0.3264 (ptm) cc_final: 0.2796 (tmm) REVERT: O 213 GLU cc_start: 0.7561 (tt0) cc_final: 0.7004 (tm-30) REVERT: M 158 ASP cc_start: 0.6764 (t0) cc_final: 0.6535 (t0) REVERT: M 265 TYR cc_start: 0.6154 (t80) cc_final: 0.5789 (t80) REVERT: N 19 GLN cc_start: 0.1362 (OUTLIER) cc_final: 0.0860 (tt0) REVERT: N 152 LEU cc_start: 0.8184 (mp) cc_final: 0.7961 (tp) REVERT: N 176 TYR cc_start: 0.4223 (m-80) cc_final: 0.3728 (m-80) REVERT: J 190 LEU cc_start: 0.7377 (tp) cc_final: 0.7039 (mm) REVERT: J 262 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6341 (mm-30) REVERT: J 265 TYR cc_start: 0.4117 (t80) cc_final: 0.3884 (t80) REVERT: J 275 ILE cc_start: 0.0350 (mm) cc_final: -0.0001 (mp) REVERT: J 276 MET cc_start: -0.0920 (mmt) cc_final: -0.1801 (mtm) REVERT: G 111 TRP cc_start: 0.7506 (p90) cc_final: 0.7141 (p90) REVERT: R 30 THR cc_start: 0.6027 (p) cc_final: 0.5742 (m) REVERT: Q 82 GLU cc_start: 0.7346 (mp0) cc_final: 0.7118 (mp0) REVERT: Q 104 TYR cc_start: 0.1153 (t80) cc_final: 0.0813 (t80) REVERT: Q 123 VAL cc_start: 0.5953 (t) cc_final: 0.5742 (t) outliers start: 4 outliers final: 0 residues processed: 368 average time/residue: 0.2007 time to fit residues: 112.9701 Evaluate side-chains 252 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 98 optimal weight: 6.9990 chunk 331 optimal weight: 40.0000 chunk 300 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 285 optimal weight: 40.0000 chunk 223 optimal weight: 20.0000 chunk 65 optimal weight: 0.0970 chunk 243 optimal weight: 6.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 124 GLN ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** N 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN R 110 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.122676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.093885 restraints weight = 110943.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.089722 restraints weight = 115276.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090564 restraints weight = 96325.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.089911 restraints weight = 83724.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090182 restraints weight = 71018.541| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 28430 Z= 0.283 Angle : 0.871 10.204 38688 Z= 0.446 Chirality : 0.052 0.300 4404 Planarity : 0.007 0.126 4960 Dihedral : 7.050 48.126 3920 Min Nonbonded Distance : 1.248 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.75 % Favored : 88.94 % Rotamer: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.14), residues: 3618 helix: -0.48 (0.18), residues: 802 sheet: -1.88 (0.16), residues: 940 loop : -1.89 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 98 TYR 0.033 0.003 TYR O 49 PHE 0.050 0.003 PHE B 64 TRP 0.046 0.003 TRP P 163 HIS 0.011 0.003 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00650 (28414) covalent geometry : angle 0.87117 (38656) SS BOND : bond 0.00791 ( 16) SS BOND : angle 1.12271 ( 32) hydrogen bonds : bond 0.04438 ( 848) hydrogen bonds : angle 6.22594 ( 2340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7704 (ptm) cc_final: 0.7498 (ptm) REVERT: E 145 ASN cc_start: 0.7810 (t0) cc_final: 0.7236 (t0) REVERT: A 172 LYS cc_start: 0.7691 (pttm) cc_final: 0.7285 (tttp) REVERT: A 183 ASP cc_start: 0.7388 (p0) cc_final: 0.7053 (p0) REVERT: A 186 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 200 MET cc_start: 0.8653 (mmm) cc_final: 0.8155 (mmm) REVERT: B 95 LEU cc_start: 0.8894 (tt) cc_final: 0.8492 (tp) REVERT: B 304 PHE cc_start: 0.7711 (m-80) cc_final: 0.7106 (m-10) REVERT: C 231 PHE cc_start: 0.8867 (t80) cc_final: 0.8316 (t80) REVERT: C 261 THR cc_start: 0.9082 (p) cc_final: 0.8657 (t) REVERT: O 42 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7253 (tm-30) REVERT: O 75 ILE cc_start: 0.6582 (mp) cc_final: 0.6241 (mm) REVERT: M 158 ASP cc_start: 0.6552 (t0) cc_final: 0.6302 (t0) REVERT: M 258 LEU cc_start: 0.1540 (mt) cc_final: 0.1249 (tp) REVERT: M 265 TYR cc_start: 0.6078 (t80) cc_final: 0.5738 (t80) REVERT: J 190 LEU cc_start: 0.7556 (tp) cc_final: 0.7273 (mm) REVERT: J 276 MET cc_start: -0.0626 (mmt) cc_final: -0.1569 (mtm) REVERT: G 12 LYS cc_start: 0.7660 (mmtt) cc_final: 0.7450 (mmtp) REVERT: R 187 TYR cc_start: 0.8156 (m-80) cc_final: 0.7951 (m-10) REVERT: Q 31 ASN cc_start: 0.6635 (t0) cc_final: 0.6351 (t0) REVERT: Q 123 VAL cc_start: 0.6260 (t) cc_final: 0.6039 (t) outliers start: 2 outliers final: 1 residues processed: 334 average time/residue: 0.1928 time to fit residues: 100.2827 Evaluate side-chains 229 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 189 optimal weight: 30.0000 chunk 357 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 321 optimal weight: 30.0000 chunk 245 optimal weight: 40.0000 chunk 234 optimal weight: 30.0000 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 311 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN C 141 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Q 59 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.123333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.094508 restraints weight = 110801.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.090635 restraints weight = 116122.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.091125 restraints weight = 86296.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.091604 restraints weight = 60552.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.091703 restraints weight = 52603.071| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.5752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 28430 Z= 0.214 Angle : 0.792 11.326 38688 Z= 0.405 Chirality : 0.050 0.243 4404 Planarity : 0.007 0.121 4960 Dihedral : 6.801 45.705 3920 Min Nonbonded Distance : 1.253 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.34 % Favored : 89.36 % Rotamer: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.14), residues: 3618 helix: -0.39 (0.18), residues: 814 sheet: -1.79 (0.17), residues: 906 loop : -1.90 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 188 TYR 0.037 0.002 TYR A 50 PHE 0.043 0.003 PHE B 64 TRP 0.031 0.002 TRP R 200 HIS 0.019 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00487 (28414) covalent geometry : angle 0.79162 (38656) SS BOND : bond 0.00396 ( 16) SS BOND : angle 1.10351 ( 32) hydrogen bonds : bond 0.03903 ( 848) hydrogen bonds : angle 5.94830 ( 2340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.7835 (ptm) cc_final: 0.7606 (ptm) REVERT: D 81 MET cc_start: 0.7489 (ptm) cc_final: 0.6099 (ppp) REVERT: E 145 ASN cc_start: 0.8042 (t0) cc_final: 0.7374 (t0) REVERT: E 147 LYS cc_start: 0.7662 (mppt) cc_final: 0.7448 (mppt) REVERT: A 172 LYS cc_start: 0.7637 (pttm) cc_final: 0.7247 (tttp) REVERT: A 183 ASP cc_start: 0.7126 (p0) cc_final: 0.6525 (p0) REVERT: B 95 LEU cc_start: 0.8726 (tt) cc_final: 0.8333 (tt) REVERT: B 276 MET cc_start: 0.8406 (mpp) cc_final: 0.7993 (mpp) REVERT: B 304 PHE cc_start: 0.7699 (m-80) cc_final: 0.6753 (m-80) REVERT: P 89 GLN cc_start: -0.0441 (OUTLIER) cc_final: -0.0646 (pp30) REVERT: P 98 PHE cc_start: 0.3562 (m-10) cc_final: 0.3294 (m-80) REVERT: O 75 ILE cc_start: 0.6452 (mp) cc_final: 0.6217 (mm) REVERT: M 158 ASP cc_start: 0.6443 (t0) cc_final: 0.6171 (t70) REVERT: M 265 TYR cc_start: 0.6073 (t80) cc_final: 0.5667 (t80) REVERT: N 254 TYR cc_start: 0.5374 (t80) cc_final: 0.5109 (t80) REVERT: J 200 MET cc_start: 0.6374 (mmt) cc_final: 0.6114 (mmt) REVERT: J 276 MET cc_start: -0.0548 (mmt) cc_final: -0.1492 (mtm) REVERT: G 12 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7428 (mmtp) REVERT: G 111 TRP cc_start: 0.7745 (p90) cc_final: 0.7341 (p90) REVERT: G 199 THR cc_start: 0.8535 (p) cc_final: 0.8101 (p) REVERT: Q 123 VAL cc_start: 0.6224 (t) cc_final: 0.6008 (t) outliers start: 2 outliers final: 0 residues processed: 337 average time/residue: 0.1912 time to fit residues: 100.4154 Evaluate side-chains 238 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 53 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 11 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 283 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 143 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN C 141 HIS ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 HIS ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN Q 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.124160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094169 restraints weight = 110714.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.090061 restraints weight = 107437.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.090558 restraints weight = 75621.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.091090 restraints weight = 55282.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.091192 restraints weight = 47430.583| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28430 Z= 0.161 Angle : 0.748 16.521 38688 Z= 0.380 Chirality : 0.049 0.203 4404 Planarity : 0.007 0.116 4960 Dihedral : 6.539 44.169 3920 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.28 % Favored : 89.50 % Rotamer: Outliers : 0.06 % Allowed : 1.36 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3618 helix: -0.15 (0.18), residues: 814 sheet: -1.71 (0.17), residues: 946 loop : -1.85 (0.15), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 96 TYR 0.047 0.002 TYR M 259 PHE 0.034 0.002 PHE B 64 TRP 0.029 0.002 TRP R 50 HIS 0.016 0.002 HIS O 91 Details of bonding type rmsd covalent geometry : bond 0.00367 (28414) covalent geometry : angle 0.74793 (38656) SS BOND : bond 0.00714 ( 16) SS BOND : angle 1.20771 ( 32) hydrogen bonds : bond 0.03695 ( 848) hydrogen bonds : angle 5.75392 ( 2340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.7823 (ptm) cc_final: 0.7567 (ptm) REVERT: D 81 MET cc_start: 0.7413 (ptm) cc_final: 0.5966 (ppp) REVERT: D 150 LEU cc_start: 0.7129 (mt) cc_final: 0.6572 (mp) REVERT: E 145 ASN cc_start: 0.7981 (t0) cc_final: 0.7400 (t0) REVERT: A 172 LYS cc_start: 0.7536 (pttm) cc_final: 0.7185 (tttp) REVERT: A 183 ASP cc_start: 0.6963 (p0) cc_final: 0.6500 (p0) REVERT: A 254 TYR cc_start: 0.8708 (t80) cc_final: 0.8272 (t80) REVERT: A 276 MET cc_start: 0.8143 (mmm) cc_final: 0.7750 (mmm) REVERT: A 295 THR cc_start: 0.5317 (m) cc_final: 0.4818 (p) REVERT: B 95 LEU cc_start: 0.8770 (tt) cc_final: 0.8302 (tp) REVERT: B 276 MET cc_start: 0.8456 (mpp) cc_final: 0.8092 (mpp) REVERT: B 304 PHE cc_start: 0.7601 (m-80) cc_final: 0.6499 (m-80) REVERT: C 168 CYS cc_start: 0.6355 (p) cc_final: 0.5840 (t) REVERT: P 98 PHE cc_start: 0.3302 (m-10) cc_final: 0.2488 (m-80) REVERT: M 198 PHE cc_start: 0.7434 (m-10) cc_final: 0.6472 (m-80) REVERT: M 218 TYR cc_start: 0.7899 (m-80) cc_final: 0.7143 (m-10) REVERT: M 265 TYR cc_start: 0.6116 (t80) cc_final: 0.5693 (t80) REVERT: J 200 MET cc_start: 0.6563 (mmt) cc_final: 0.6298 (mmt) REVERT: J 254 TYR cc_start: 0.5566 (t80) cc_final: 0.5351 (t80) REVERT: J 276 MET cc_start: -0.0489 (mmt) cc_final: -0.1434 (mtm) REVERT: G 111 TRP cc_start: 0.7645 (p90) cc_final: 0.7192 (p90) REVERT: G 199 THR cc_start: 0.8611 (p) cc_final: 0.8193 (p) REVERT: R 30 THR cc_start: 0.5888 (p) cc_final: 0.5581 (m) REVERT: R 187 TYR cc_start: 0.8259 (m-80) cc_final: 0.8042 (m-10) REVERT: Q 82 GLU cc_start: 0.7312 (mp0) cc_final: 0.6879 (mp0) REVERT: Q 123 VAL cc_start: 0.6270 (t) cc_final: 0.6047 (t) REVERT: Q 155 LYS cc_start: 0.7660 (mttt) cc_final: 0.7459 (mtmt) outliers start: 2 outliers final: 0 residues processed: 325 average time/residue: 0.1954 time to fit residues: 98.5333 Evaluate side-chains 230 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 263 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 334 optimal weight: 40.0000 chunk 247 optimal weight: 8.9990 chunk 230 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 245 optimal weight: 30.0000 chunk 208 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN E 212 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN N 143 GLN ** N 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 167 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.120355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.091123 restraints weight = 109097.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.085743 restraints weight = 114287.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.086422 restraints weight = 104791.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.086016 restraints weight = 81655.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.086415 restraints weight = 66689.002| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.215 28430 Z= 0.403 Angle : 1.004 13.975 38688 Z= 0.515 Chirality : 0.057 0.347 4404 Planarity : 0.008 0.139 4960 Dihedral : 7.069 45.779 3920 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.49 % Favored : 87.18 % Rotamer: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.14), residues: 3618 helix: -0.98 (0.17), residues: 844 sheet: -1.68 (0.18), residues: 868 loop : -2.18 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 98 TYR 0.030 0.003 TYR C 265 PHE 0.036 0.004 PHE B 64 TRP 0.044 0.004 TRP M 122 HIS 0.019 0.004 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00914 (28414) covalent geometry : angle 1.00368 (38656) SS BOND : bond 0.00504 ( 16) SS BOND : angle 1.49226 ( 32) hydrogen bonds : bond 0.05137 ( 848) hydrogen bonds : angle 6.52649 ( 2340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8104 (mmmm) REVERT: D 48 MET cc_start: 0.8101 (ptm) cc_final: 0.7893 (ptm) REVERT: D 81 MET cc_start: 0.7841 (ptm) cc_final: 0.7101 (ppp) REVERT: D 119 THR cc_start: 0.7844 (p) cc_final: 0.7560 (p) REVERT: D 150 LEU cc_start: 0.7239 (mt) cc_final: 0.6625 (mp) REVERT: E 145 ASN cc_start: 0.7707 (t0) cc_final: 0.6345 (t0) REVERT: A 172 LYS cc_start: 0.7911 (pttm) cc_final: 0.7479 (tttp) REVERT: B 212 MET cc_start: 0.8630 (mmm) cc_final: 0.8321 (mtp) REVERT: C 231 PHE cc_start: 0.9056 (t80) cc_final: 0.8834 (t80) REVERT: C 261 THR cc_start: 0.9097 (p) cc_final: 0.8755 (t) REVERT: C 278 VAL cc_start: 0.9273 (t) cc_final: 0.8927 (p) REVERT: P 98 PHE cc_start: 0.3324 (m-10) cc_final: 0.2558 (m-80) REVERT: M 111 HIS cc_start: 0.2900 (t-170) cc_final: 0.2262 (m90) REVERT: J 200 MET cc_start: 0.6497 (mmt) cc_final: 0.6241 (mmt) REVERT: J 254 TYR cc_start: 0.5877 (t80) cc_final: 0.5544 (t80) REVERT: J 276 MET cc_start: -0.0211 (mmt) cc_final: -0.1182 (mtm) REVERT: R 10 GLU cc_start: 0.6254 (mp0) cc_final: 0.6046 (mp0) REVERT: R 30 THR cc_start: 0.6247 (p) cc_final: 0.5921 (m) REVERT: R 59 ASN cc_start: 0.5619 (t0) cc_final: 0.5205 (t0) REVERT: R 105 ARG cc_start: 0.4144 (mpt-90) cc_final: 0.3803 (mtt90) REVERT: R 158 PHE cc_start: 0.8413 (t80) cc_final: 0.8027 (t80) REVERT: R 187 TYR cc_start: 0.8451 (m-80) cc_final: 0.8172 (m-10) REVERT: Q 64 LEU cc_start: 0.8657 (mt) cc_final: 0.8363 (mp) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.1926 time to fit residues: 87.1859 Evaluate side-chains 221 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 150 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 241 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 338 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 144 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 ASN E 157 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 90 ASN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN C 79 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN P 90 GLN ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 ASN ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN R 6 GLN R 110 ASN Q 59 ASN ** Q 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.124260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.095185 restraints weight = 110929.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.091380 restraints weight = 113424.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.091922 restraints weight = 81055.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.092403 restraints weight = 58561.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092561 restraints weight = 50536.615| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28430 Z= 0.150 Angle : 0.781 14.639 38688 Z= 0.395 Chirality : 0.049 0.238 4404 Planarity : 0.007 0.116 4960 Dihedral : 6.556 44.661 3920 Min Nonbonded Distance : 1.360 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.56 % Favored : 90.22 % Rotamer: Outliers : 0.10 % Allowed : 0.58 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3618 helix: -0.16 (0.18), residues: 808 sheet: -1.75 (0.17), residues: 982 loop : -1.88 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 188 TYR 0.042 0.002 TYR P 49 PHE 0.033 0.002 PHE M 304 TRP 0.033 0.002 TRP M 122 HIS 0.013 0.001 HIS J 187 Details of bonding type rmsd covalent geometry : bond 0.00338 (28414) covalent geometry : angle 0.78058 (38656) SS BOND : bond 0.00504 ( 16) SS BOND : angle 1.09358 ( 32) hydrogen bonds : bond 0.03694 ( 848) hydrogen bonds : angle 5.75499 ( 2340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 312 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8001 (ptm) cc_final: 0.7724 (ptm) REVERT: D 81 MET cc_start: 0.7618 (ptm) cc_final: 0.6985 (ppp) REVERT: D 119 THR cc_start: 0.7572 (p) cc_final: 0.7280 (p) REVERT: D 150 LEU cc_start: 0.7053 (mt) cc_final: 0.6475 (mp) REVERT: E 94 LEU cc_start: 0.8691 (mt) cc_final: 0.8467 (mt) REVERT: A 8 ILE cc_start: 0.6867 (mp) cc_final: 0.6607 (mt) REVERT: A 55 PHE cc_start: 0.6115 (m-10) cc_final: 0.5882 (m-10) REVERT: A 172 LYS cc_start: 0.7601 (pttm) cc_final: 0.7301 (tttm) REVERT: A 212 MET cc_start: 0.7283 (mmm) cc_final: 0.6838 (tpp) REVERT: A 254 TYR cc_start: 0.8727 (t80) cc_final: 0.8392 (t80) REVERT: A 259 TYR cc_start: 0.8463 (t80) cc_final: 0.7611 (t80) REVERT: A 276 MET cc_start: 0.8076 (mmm) cc_final: 0.7682 (mmm) REVERT: B 19 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8810 (pp30) REVERT: B 276 MET cc_start: 0.8320 (mpp) cc_final: 0.8103 (mpp) REVERT: B 304 PHE cc_start: 0.7935 (m-80) cc_final: 0.6904 (m-10) REVERT: C 174 ILE cc_start: 0.6723 (tt) cc_final: 0.6330 (mt) REVERT: C 276 MET cc_start: 0.8487 (mpp) cc_final: 0.7481 (mtt) REVERT: C 278 VAL cc_start: 0.9249 (t) cc_final: 0.8969 (p) REVERT: P 98 PHE cc_start: 0.3780 (m-10) cc_final: 0.2860 (m-80) REVERT: O 61 ARG cc_start: 0.7398 (tpt90) cc_final: 0.7063 (mmm160) REVERT: M 198 PHE cc_start: 0.7573 (m-10) cc_final: 0.6847 (m-80) REVERT: J 97 LEU cc_start: 0.2912 (pp) cc_final: 0.2649 (tt) REVERT: J 200 MET cc_start: 0.6247 (mmt) cc_final: 0.4844 (mmt) REVERT: J 276 MET cc_start: -0.0477 (mmt) cc_final: -0.1035 (mmp) REVERT: G 111 TRP cc_start: 0.7750 (p90) cc_final: 0.7187 (p90) REVERT: R 30 THR cc_start: 0.6012 (p) cc_final: 0.5723 (m) REVERT: R 59 ASN cc_start: 0.5573 (t0) cc_final: 0.5291 (t0) REVERT: R 187 TYR cc_start: 0.8432 (m-80) cc_final: 0.8211 (m-10) REVERT: Q 64 LEU cc_start: 0.8421 (mt) cc_final: 0.8124 (mp) REVERT: Q 82 GLU cc_start: 0.7395 (mp0) cc_final: 0.7087 (mp0) outliers start: 3 outliers final: 1 residues processed: 314 average time/residue: 0.1915 time to fit residues: 93.7655 Evaluate side-chains 222 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 311 optimal weight: 0.0370 chunk 322 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 173 optimal weight: 10.0000 overall best weight: 2.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 GLN ** P 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Q 59 ASN ** Q 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.122517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.094512 restraints weight = 110330.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.091091 restraints weight = 122369.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.091297 restraints weight = 99733.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.091331 restraints weight = 79022.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.091540 restraints weight = 64992.843| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 28430 Z= 0.228 Angle : 0.835 11.037 38688 Z= 0.425 Chirality : 0.051 0.268 4404 Planarity : 0.007 0.121 4960 Dihedral : 6.576 42.353 3920 Min Nonbonded Distance : 1.305 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.22 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 3618 helix: -0.18 (0.18), residues: 790 sheet: -1.65 (0.17), residues: 938 loop : -1.92 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 67 TYR 0.041 0.002 TYR P 49 PHE 0.044 0.003 PHE O 71 TRP 0.035 0.003 TRP M 122 HIS 0.013 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00525 (28414) covalent geometry : angle 0.83479 (38656) SS BOND : bond 0.00362 ( 16) SS BOND : angle 1.12770 ( 32) hydrogen bonds : bond 0.04152 ( 848) hydrogen bonds : angle 5.96326 ( 2340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 MET cc_start: 0.8015 (ptm) cc_final: 0.7692 (ptt) REVERT: D 81 MET cc_start: 0.7708 (ptm) cc_final: 0.7099 (ppp) REVERT: D 119 THR cc_start: 0.7675 (p) cc_final: 0.7353 (p) REVERT: E 145 ASN cc_start: 0.7436 (p0) cc_final: 0.7014 (p0) REVERT: A 55 PHE cc_start: 0.5890 (m-10) cc_final: 0.5665 (m-10) REVERT: A 172 LYS cc_start: 0.7530 (pttm) cc_final: 0.7235 (ttpp) REVERT: A 212 MET cc_start: 0.7224 (mmm) cc_final: 0.6907 (mmm) REVERT: A 276 MET cc_start: 0.8012 (mmm) cc_final: 0.7650 (mmm) REVERT: B 212 MET cc_start: 0.8605 (mmm) cc_final: 0.8323 (mtp) REVERT: B 304 PHE cc_start: 0.8011 (m-80) cc_final: 0.7526 (m-10) REVERT: C 261 THR cc_start: 0.9049 (p) cc_final: 0.8570 (t) REVERT: C 276 MET cc_start: 0.8450 (mpp) cc_final: 0.7741 (mtt) REVERT: C 278 VAL cc_start: 0.9347 (t) cc_final: 0.9063 (p) REVERT: P 98 PHE cc_start: 0.3686 (m-10) cc_final: 0.2732 (m-80) REVERT: O 61 ARG cc_start: 0.7271 (tpt90) cc_final: 0.6705 (tpt90) REVERT: O 94 LEU cc_start: 0.6638 (mm) cc_final: 0.6095 (mt) REVERT: O 156 GLN cc_start: 0.5154 (mp-120) cc_final: 0.4785 (pm20) REVERT: M 198 PHE cc_start: 0.7460 (m-10) cc_final: 0.6796 (m-80) REVERT: M 212 MET cc_start: 0.3113 (mtt) cc_final: 0.2883 (mtt) REVERT: J 200 MET cc_start: 0.6200 (mmt) cc_final: 0.5878 (mmt) REVERT: R 30 THR cc_start: 0.6054 (p) cc_final: 0.5782 (m) REVERT: R 59 ASN cc_start: 0.5588 (t0) cc_final: 0.5324 (t0) REVERT: Q 64 LEU cc_start: 0.8384 (mt) cc_final: 0.8042 (mp) REVERT: Q 82 GLU cc_start: 0.7336 (mp0) cc_final: 0.7036 (mp0) REVERT: Q 123 VAL cc_start: 0.6467 (t) cc_final: 0.6257 (t) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1909 time to fit residues: 83.9256 Evaluate side-chains 209 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 276 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 238 optimal weight: 4.9990 chunk 339 optimal weight: 30.0000 chunk 286 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 ASN ** Q 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.123476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.095268 restraints weight = 111239.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.091539 restraints weight = 120999.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.091966 restraints weight = 86002.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092434 restraints weight = 61775.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.092563 restraints weight = 53968.577| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28430 Z= 0.158 Angle : 0.774 11.258 38688 Z= 0.392 Chirality : 0.049 0.271 4404 Planarity : 0.007 0.116 4960 Dihedral : 6.401 43.657 3920 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.28 % Favored : 89.52 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.53 % Twisted Proline : 1.74 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3618 helix: 0.03 (0.18), residues: 796 sheet: -1.61 (0.17), residues: 966 loop : -1.79 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 180 TYR 0.037 0.002 TYR P 49 PHE 0.042 0.002 PHE O 71 TRP 0.027 0.002 TRP R 200 HIS 0.013 0.002 HIS J 187 Details of bonding type rmsd covalent geometry : bond 0.00363 (28414) covalent geometry : angle 0.77406 (38656) SS BOND : bond 0.00325 ( 16) SS BOND : angle 1.07295 ( 32) hydrogen bonds : bond 0.03686 ( 848) hydrogen bonds : angle 5.75835 ( 2340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4566.55 seconds wall clock time: 80 minutes 28.30 seconds (4828.30 seconds total)